Multiple sequence alignment - TraesCS3B01G247700

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3B01G247700 chr3B 100.000 2888 0 0 1 2888 394089882 394086995 0.000000e+00 5334
1 TraesCS3B01G247700 chr3B 90.154 518 39 7 2123 2637 42150076 42150584 0.000000e+00 664
2 TraesCS3B01G247700 chr3B 94.194 310 18 0 391 700 731003135 731002826 9.370000e-130 473
3 TraesCS3B01G247700 chr3D 92.398 1447 42 25 699 2116 298584843 298583436 0.000000e+00 2001
4 TraesCS3B01G247700 chr3D 90.170 763 65 4 2129 2888 564804434 564803679 0.000000e+00 985
5 TraesCS3B01G247700 chr3D 96.535 404 13 1 1 403 298585248 298584845 0.000000e+00 667
6 TraesCS3B01G247700 chr3A 92.201 1436 48 21 699 2115 396611569 396610179 0.000000e+00 1973
7 TraesCS3B01G247700 chr3A 95.792 404 16 1 1 403 396611974 396611571 0.000000e+00 651
8 TraesCS3B01G247700 chr1B 94.003 767 36 3 2123 2888 654045158 654044401 0.000000e+00 1153
9 TraesCS3B01G247700 chr1B 93.090 767 43 3 2123 2888 581165594 581166351 0.000000e+00 1114
10 TraesCS3B01G247700 chr1B 84.453 759 103 10 2136 2888 559109215 559108466 0.000000e+00 734
11 TraesCS3B01G247700 chr1B 83.531 759 110 11 2136 2888 429966692 429967441 0.000000e+00 695
12 TraesCS3B01G247700 chr1B 87.478 559 55 8 2331 2888 296761487 296762031 5.250000e-177 630
13 TraesCS3B01G247700 chr1B 90.365 384 27 4 2506 2888 492859950 492859576 2.000000e-136 496
14 TraesCS3B01G247700 chr6B 92.568 767 47 3 2123 2888 691335945 691336702 0.000000e+00 1092
15 TraesCS3B01G247700 chr6B 94.983 299 15 0 401 699 538068040 538067742 1.210000e-128 470
16 TraesCS3B01G247700 chr6A 89.515 763 69 6 2129 2888 73786304 73785550 0.000000e+00 955
17 TraesCS3B01G247700 chr4A 91.544 544 36 3 2346 2888 698361971 698361437 0.000000e+00 741
18 TraesCS3B01G247700 chr5B 95.323 449 20 1 2123 2571 586455575 586456022 0.000000e+00 712
19 TraesCS3B01G247700 chr5B 90.741 432 27 7 2459 2888 586456012 586456432 5.400000e-157 564
20 TraesCS3B01G247700 chr5B 94.444 306 16 1 402 706 447699089 447698784 1.210000e-128 470
21 TraesCS3B01G247700 chr5B 95.000 300 14 1 401 699 709172009 709171710 1.210000e-128 470
22 TraesCS3B01G247700 chr5A 95.973 298 12 0 402 699 439570425 439570128 4.330000e-133 484
23 TraesCS3B01G247700 chr7B 95.098 306 14 1 402 706 29238013 29237708 5.600000e-132 481
24 TraesCS3B01G247700 chr4B 94.754 305 15 1 404 708 621443578 621443881 9.370000e-130 473
25 TraesCS3B01G247700 chr4B 94.118 306 17 1 401 706 54083039 54082735 5.640000e-127 464
26 TraesCS3B01G247700 chr2B 93.569 311 19 1 391 701 480355292 480355601 2.030000e-126 462


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G247700 chr3B 394086995 394089882 2887 True 5334 5334 100.0000 1 2888 1 chr3B.!!$R1 2887
1 TraesCS3B01G247700 chr3B 42150076 42150584 508 False 664 664 90.1540 2123 2637 1 chr3B.!!$F1 514
2 TraesCS3B01G247700 chr3D 298583436 298585248 1812 True 1334 2001 94.4665 1 2116 2 chr3D.!!$R2 2115
3 TraesCS3B01G247700 chr3D 564803679 564804434 755 True 985 985 90.1700 2129 2888 1 chr3D.!!$R1 759
4 TraesCS3B01G247700 chr3A 396610179 396611974 1795 True 1312 1973 93.9965 1 2115 2 chr3A.!!$R1 2114
5 TraesCS3B01G247700 chr1B 654044401 654045158 757 True 1153 1153 94.0030 2123 2888 1 chr1B.!!$R3 765
6 TraesCS3B01G247700 chr1B 581165594 581166351 757 False 1114 1114 93.0900 2123 2888 1 chr1B.!!$F3 765
7 TraesCS3B01G247700 chr1B 559108466 559109215 749 True 734 734 84.4530 2136 2888 1 chr1B.!!$R2 752
8 TraesCS3B01G247700 chr1B 429966692 429967441 749 False 695 695 83.5310 2136 2888 1 chr1B.!!$F2 752
9 TraesCS3B01G247700 chr1B 296761487 296762031 544 False 630 630 87.4780 2331 2888 1 chr1B.!!$F1 557
10 TraesCS3B01G247700 chr6B 691335945 691336702 757 False 1092 1092 92.5680 2123 2888 1 chr6B.!!$F1 765
11 TraesCS3B01G247700 chr6A 73785550 73786304 754 True 955 955 89.5150 2129 2888 1 chr6A.!!$R1 759
12 TraesCS3B01G247700 chr4A 698361437 698361971 534 True 741 741 91.5440 2346 2888 1 chr4A.!!$R1 542
13 TraesCS3B01G247700 chr5B 586455575 586456432 857 False 638 712 93.0320 2123 2888 2 chr5B.!!$F1 765

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
581 583 0.034756 AACACGACATGCAGTGGCTA 59.965 50.0 20.6 0.0 42.25 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2118 2163 0.030092 TCCCTCCCCAAATCCGATCT 60.03 55.0 0.0 0.0 0.0 2.75 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 6.149575 CTTTCCCTAAGATAAAGCAGCAGCT 61.150 44.000 0.00 0.00 44.54 4.24
209 211 0.661020 ACGCAAAACCTGAACTTCGG 59.339 50.000 0.00 0.00 0.00 4.30
237 239 1.765314 ACATGTGGACCTCATAGCTCC 59.235 52.381 8.69 0.00 0.00 4.70
280 282 0.597898 TGCGCGTGCTTGTACTTGTA 60.598 50.000 23.16 0.00 43.34 2.41
293 295 2.094762 ACTTGTAGCCGAAGCGAATT 57.905 45.000 0.00 0.00 46.67 2.17
314 316 1.952263 GCCTTTTGCGCTCTCTTGT 59.048 52.632 9.73 0.00 0.00 3.16
386 388 4.837972 ACAAATCTCTTCTCTTACTGGCC 58.162 43.478 0.00 0.00 0.00 5.36
401 403 0.708209 TGGCCAGTCTGGTACTCCTA 59.292 55.000 20.24 0.00 40.46 2.94
402 404 1.342076 TGGCCAGTCTGGTACTCCTAG 60.342 57.143 20.24 0.00 40.46 3.02
403 405 1.342175 GGCCAGTCTGGTACTCCTAGT 60.342 57.143 20.24 0.00 40.46 2.57
404 406 2.091994 GGCCAGTCTGGTACTCCTAGTA 60.092 54.545 20.24 0.00 40.46 1.82
413 415 3.124578 GTACTCCTAGTACTCCCTCCG 57.875 57.143 0.00 0.00 45.70 4.63
414 416 1.594129 ACTCCTAGTACTCCCTCCGT 58.406 55.000 0.00 0.00 0.00 4.69
415 417 1.490069 ACTCCTAGTACTCCCTCCGTC 59.510 57.143 0.00 0.00 0.00 4.79
416 418 1.770061 CTCCTAGTACTCCCTCCGTCT 59.230 57.143 0.00 0.00 0.00 4.18
417 419 2.971330 CTCCTAGTACTCCCTCCGTCTA 59.029 54.545 0.00 0.00 0.00 2.59
418 420 2.971330 TCCTAGTACTCCCTCCGTCTAG 59.029 54.545 0.00 0.00 0.00 2.43
419 421 2.038820 CCTAGTACTCCCTCCGTCTAGG 59.961 59.091 0.00 0.00 38.64 3.02
420 422 1.594129 AGTACTCCCTCCGTCTAGGT 58.406 55.000 0.00 0.00 41.99 3.08
421 423 1.212441 AGTACTCCCTCCGTCTAGGTG 59.788 57.143 0.00 0.00 41.99 4.00
422 424 1.064832 GTACTCCCTCCGTCTAGGTGT 60.065 57.143 0.00 0.00 41.99 4.16
423 425 0.323542 ACTCCCTCCGTCTAGGTGTG 60.324 60.000 0.00 0.00 41.99 3.82
424 426 0.323542 CTCCCTCCGTCTAGGTGTGT 60.324 60.000 0.00 0.00 41.99 3.72
425 427 0.994247 TCCCTCCGTCTAGGTGTGTA 59.006 55.000 0.00 0.00 41.99 2.90
426 428 1.355381 TCCCTCCGTCTAGGTGTGTAA 59.645 52.381 0.00 0.00 41.99 2.41
427 429 1.749634 CCCTCCGTCTAGGTGTGTAAG 59.250 57.143 0.00 0.00 41.99 2.34
428 430 2.444421 CCTCCGTCTAGGTGTGTAAGT 58.556 52.381 0.00 0.00 41.99 2.24
429 431 2.422832 CCTCCGTCTAGGTGTGTAAGTC 59.577 54.545 0.00 0.00 41.99 3.01
430 432 3.079578 CTCCGTCTAGGTGTGTAAGTCA 58.920 50.000 0.00 0.00 41.99 3.41
431 433 3.693807 TCCGTCTAGGTGTGTAAGTCAT 58.306 45.455 0.00 0.00 41.99 3.06
432 434 3.693085 TCCGTCTAGGTGTGTAAGTCATC 59.307 47.826 0.00 0.00 41.99 2.92
433 435 3.695060 CCGTCTAGGTGTGTAAGTCATCT 59.305 47.826 0.00 0.00 34.51 2.90
434 436 4.158025 CCGTCTAGGTGTGTAAGTCATCTT 59.842 45.833 0.00 0.00 35.02 2.40
435 437 5.356190 CCGTCTAGGTGTGTAAGTCATCTTA 59.644 44.000 0.00 0.00 33.66 2.10
436 438 6.039493 CCGTCTAGGTGTGTAAGTCATCTTAT 59.961 42.308 0.00 0.00 35.59 1.73
437 439 6.913132 CGTCTAGGTGTGTAAGTCATCTTATG 59.087 42.308 0.00 0.00 38.25 1.90
438 440 7.201705 CGTCTAGGTGTGTAAGTCATCTTATGA 60.202 40.741 0.00 0.00 38.25 2.15
439 441 8.467598 GTCTAGGTGTGTAAGTCATCTTATGAA 58.532 37.037 0.00 0.00 41.69 2.57
440 442 9.031537 TCTAGGTGTGTAAGTCATCTTATGAAA 57.968 33.333 0.00 0.00 41.69 2.69
441 443 9.653287 CTAGGTGTGTAAGTCATCTTATGAAAA 57.347 33.333 0.00 0.00 41.69 2.29
442 444 8.324163 AGGTGTGTAAGTCATCTTATGAAAAC 57.676 34.615 0.00 0.00 41.69 2.43
443 445 7.390718 AGGTGTGTAAGTCATCTTATGAAAACC 59.609 37.037 0.00 0.00 41.69 3.27
444 446 7.174253 GGTGTGTAAGTCATCTTATGAAAACCA 59.826 37.037 0.00 0.00 41.69 3.67
445 447 8.564574 GTGTGTAAGTCATCTTATGAAAACCAA 58.435 33.333 0.00 0.00 41.69 3.67
446 448 9.126151 TGTGTAAGTCATCTTATGAAAACCAAA 57.874 29.630 0.00 0.00 41.69 3.28
453 455 9.750125 GTCATCTTATGAAAACCAAATAATCCC 57.250 33.333 0.00 0.00 41.69 3.85
454 456 9.486123 TCATCTTATGAAAACCAAATAATCCCA 57.514 29.630 0.00 0.00 36.11 4.37
460 462 7.793927 TGAAAACCAAATAATCCCAAAACAC 57.206 32.000 0.00 0.00 0.00 3.32
461 463 7.569240 TGAAAACCAAATAATCCCAAAACACT 58.431 30.769 0.00 0.00 0.00 3.55
462 464 8.049721 TGAAAACCAAATAATCCCAAAACACTT 58.950 29.630 0.00 0.00 0.00 3.16
463 465 9.549078 GAAAACCAAATAATCCCAAAACACTTA 57.451 29.630 0.00 0.00 0.00 2.24
464 466 9.554395 AAAACCAAATAATCCCAAAACACTTAG 57.446 29.630 0.00 0.00 0.00 2.18
465 467 7.239763 ACCAAATAATCCCAAAACACTTAGG 57.760 36.000 0.00 0.00 0.00 2.69
466 468 6.106003 CCAAATAATCCCAAAACACTTAGGC 58.894 40.000 0.00 0.00 0.00 3.93
467 469 5.576447 AATAATCCCAAAACACTTAGGCG 57.424 39.130 0.00 0.00 0.00 5.52
468 470 1.173913 ATCCCAAAACACTTAGGCGC 58.826 50.000 0.00 0.00 0.00 6.53
469 471 1.209127 CCCAAAACACTTAGGCGCG 59.791 57.895 0.00 0.00 0.00 6.86
470 472 1.209127 CCAAAACACTTAGGCGCGG 59.791 57.895 8.83 0.00 0.00 6.46
471 473 1.512156 CCAAAACACTTAGGCGCGGT 61.512 55.000 8.83 0.00 0.00 5.68
472 474 0.385473 CAAAACACTTAGGCGCGGTG 60.385 55.000 8.83 9.75 37.05 4.94
473 475 2.125202 AAAACACTTAGGCGCGGTGC 62.125 55.000 8.83 4.64 45.38 5.01
486 488 4.354725 GCGCGGTGCATTAAATTTTATC 57.645 40.909 8.83 0.00 45.45 1.75
487 489 4.041723 GCGCGGTGCATTAAATTTTATCT 58.958 39.130 8.83 0.00 45.45 1.98
488 490 4.146443 GCGCGGTGCATTAAATTTTATCTC 59.854 41.667 8.83 0.00 45.45 2.75
489 491 4.375698 CGCGGTGCATTAAATTTTATCTCG 59.624 41.667 0.00 0.00 0.00 4.04
490 492 5.270853 GCGGTGCATTAAATTTTATCTCGT 58.729 37.500 0.00 0.00 0.00 4.18
491 493 5.741982 GCGGTGCATTAAATTTTATCTCGTT 59.258 36.000 0.00 0.00 0.00 3.85
492 494 6.252655 GCGGTGCATTAAATTTTATCTCGTTT 59.747 34.615 0.00 0.00 0.00 3.60
493 495 7.201401 GCGGTGCATTAAATTTTATCTCGTTTT 60.201 33.333 0.00 0.00 0.00 2.43
494 496 8.643752 CGGTGCATTAAATTTTATCTCGTTTTT 58.356 29.630 0.00 0.00 0.00 1.94
517 519 9.829507 TTTTTGTTTCTTGACATATCAACCAAT 57.170 25.926 0.00 0.00 40.01 3.16
521 523 9.513906 TGTTTCTTGACATATCAACCAATAAGA 57.486 29.630 0.00 0.00 40.01 2.10
530 532 8.284945 CATATCAACCAATAAGATATGTGGGG 57.715 38.462 11.54 0.00 43.08 4.96
531 533 5.725551 TCAACCAATAAGATATGTGGGGT 57.274 39.130 0.00 0.00 35.32 4.95
532 534 5.445069 TCAACCAATAAGATATGTGGGGTG 58.555 41.667 0.00 0.00 35.32 4.61
533 535 5.044476 TCAACCAATAAGATATGTGGGGTGT 60.044 40.000 0.00 0.00 35.32 4.16
534 536 6.158871 TCAACCAATAAGATATGTGGGGTGTA 59.841 38.462 0.00 0.00 35.32 2.90
535 537 5.937111 ACCAATAAGATATGTGGGGTGTAC 58.063 41.667 0.00 0.00 35.32 2.90
536 538 5.430417 ACCAATAAGATATGTGGGGTGTACA 59.570 40.000 0.00 0.00 35.32 2.90
537 539 6.102615 ACCAATAAGATATGTGGGGTGTACAT 59.897 38.462 0.00 0.00 41.36 2.29
538 540 6.430925 CCAATAAGATATGTGGGGTGTACATG 59.569 42.308 0.00 0.00 39.03 3.21
539 541 6.763715 ATAAGATATGTGGGGTGTACATGT 57.236 37.500 2.69 2.69 39.03 3.21
540 542 5.450818 AAGATATGTGGGGTGTACATGTT 57.549 39.130 2.30 0.00 39.03 2.71
541 543 5.450818 AGATATGTGGGGTGTACATGTTT 57.549 39.130 2.30 0.00 39.03 2.83
542 544 5.826643 AGATATGTGGGGTGTACATGTTTT 58.173 37.500 2.30 0.00 39.03 2.43
543 545 6.252995 AGATATGTGGGGTGTACATGTTTTT 58.747 36.000 2.30 0.00 39.03 1.94
544 546 7.406916 AGATATGTGGGGTGTACATGTTTTTA 58.593 34.615 2.30 0.00 39.03 1.52
545 547 7.891183 AGATATGTGGGGTGTACATGTTTTTAA 59.109 33.333 2.30 0.00 39.03 1.52
546 548 6.926630 ATGTGGGGTGTACATGTTTTTAAT 57.073 33.333 2.30 0.00 37.38 1.40
547 549 6.090483 TGTGGGGTGTACATGTTTTTAATG 57.910 37.500 2.30 0.00 0.00 1.90
548 550 5.833667 TGTGGGGTGTACATGTTTTTAATGA 59.166 36.000 2.30 0.00 0.00 2.57
549 551 6.153756 GTGGGGTGTACATGTTTTTAATGAC 58.846 40.000 2.30 0.00 0.00 3.06
550 552 6.015772 GTGGGGTGTACATGTTTTTAATGACT 60.016 38.462 2.30 0.00 0.00 3.41
551 553 6.551601 TGGGGTGTACATGTTTTTAATGACTT 59.448 34.615 2.30 0.00 0.00 3.01
552 554 6.866248 GGGGTGTACATGTTTTTAATGACTTG 59.134 38.462 2.30 4.21 0.00 3.16
553 555 7.255660 GGGGTGTACATGTTTTTAATGACTTGA 60.256 37.037 2.30 0.00 0.00 3.02
554 556 7.807907 GGGTGTACATGTTTTTAATGACTTGAG 59.192 37.037 2.30 0.00 0.00 3.02
555 557 8.564574 GGTGTACATGTTTTTAATGACTTGAGA 58.435 33.333 2.30 0.00 0.00 3.27
556 558 9.382244 GTGTACATGTTTTTAATGACTTGAGAC 57.618 33.333 2.30 0.00 0.00 3.36
557 559 9.337396 TGTACATGTTTTTAATGACTTGAGACT 57.663 29.630 2.30 0.00 0.00 3.24
560 562 8.784043 ACATGTTTTTAATGACTTGAGACTACC 58.216 33.333 0.00 0.00 0.00 3.18
561 563 8.783093 CATGTTTTTAATGACTTGAGACTACCA 58.217 33.333 0.00 0.00 0.00 3.25
562 564 8.740123 TGTTTTTAATGACTTGAGACTACCAA 57.260 30.769 0.00 0.00 0.00 3.67
563 565 9.179909 TGTTTTTAATGACTTGAGACTACCAAA 57.820 29.630 0.00 0.00 0.00 3.28
564 566 9.447040 GTTTTTAATGACTTGAGACTACCAAAC 57.553 33.333 0.00 0.00 0.00 2.93
565 567 8.740123 TTTTAATGACTTGAGACTACCAAACA 57.260 30.769 0.00 0.00 0.00 2.83
566 568 7.724305 TTAATGACTTGAGACTACCAAACAC 57.276 36.000 0.00 0.00 0.00 3.32
567 569 3.713288 TGACTTGAGACTACCAAACACG 58.287 45.455 0.00 0.00 0.00 4.49
568 570 3.382227 TGACTTGAGACTACCAAACACGA 59.618 43.478 0.00 0.00 0.00 4.35
569 571 3.714391 ACTTGAGACTACCAAACACGAC 58.286 45.455 0.00 0.00 0.00 4.34
570 572 3.131577 ACTTGAGACTACCAAACACGACA 59.868 43.478 0.00 0.00 0.00 4.35
571 573 4.202223 ACTTGAGACTACCAAACACGACAT 60.202 41.667 0.00 0.00 0.00 3.06
572 574 3.649073 TGAGACTACCAAACACGACATG 58.351 45.455 0.00 0.00 0.00 3.21
573 575 2.412089 GAGACTACCAAACACGACATGC 59.588 50.000 0.00 0.00 0.00 4.06
574 576 2.139917 GACTACCAAACACGACATGCA 58.860 47.619 0.00 0.00 0.00 3.96
575 577 2.143122 ACTACCAAACACGACATGCAG 58.857 47.619 0.00 0.00 0.00 4.41
576 578 2.143122 CTACCAAACACGACATGCAGT 58.857 47.619 0.00 0.00 0.00 4.40
577 579 0.662619 ACCAAACACGACATGCAGTG 59.337 50.000 16.62 16.62 43.46 3.66
578 580 0.040157 CCAAACACGACATGCAGTGG 60.040 55.000 20.60 3.36 42.25 4.00
579 581 0.661187 CAAACACGACATGCAGTGGC 60.661 55.000 20.60 0.92 42.25 5.01
580 582 0.819259 AAACACGACATGCAGTGGCT 60.819 50.000 20.60 8.47 42.25 4.75
581 583 0.034756 AACACGACATGCAGTGGCTA 59.965 50.000 20.60 0.00 42.25 3.93
582 584 0.390340 ACACGACATGCAGTGGCTAG 60.390 55.000 20.60 0.00 42.25 3.42
583 585 0.390340 CACGACATGCAGTGGCTAGT 60.390 55.000 11.93 0.00 41.91 2.57
584 586 0.321671 ACGACATGCAGTGGCTAGTT 59.678 50.000 0.00 0.00 41.91 2.24
585 587 1.002366 CGACATGCAGTGGCTAGTTC 58.998 55.000 0.00 0.00 41.91 3.01
586 588 1.672737 CGACATGCAGTGGCTAGTTCA 60.673 52.381 0.00 0.00 41.91 3.18
587 589 2.636830 GACATGCAGTGGCTAGTTCAT 58.363 47.619 0.00 0.00 41.91 2.57
588 590 3.012518 GACATGCAGTGGCTAGTTCATT 58.987 45.455 0.00 0.00 41.91 2.57
589 591 2.751259 ACATGCAGTGGCTAGTTCATTG 59.249 45.455 0.00 0.00 41.91 2.82
590 592 1.167851 TGCAGTGGCTAGTTCATTGC 58.832 50.000 20.28 20.28 44.56 3.56
591 593 1.167851 GCAGTGGCTAGTTCATTGCA 58.832 50.000 21.35 0.00 44.01 4.08
592 594 1.747355 GCAGTGGCTAGTTCATTGCAT 59.253 47.619 21.35 0.00 44.01 3.96
593 595 2.479049 GCAGTGGCTAGTTCATTGCATG 60.479 50.000 21.35 0.00 44.01 4.06
594 596 1.747355 AGTGGCTAGTTCATTGCATGC 59.253 47.619 11.82 11.82 0.00 4.06
595 597 1.473677 GTGGCTAGTTCATTGCATGCA 59.526 47.619 18.46 18.46 0.00 3.96
596 598 2.094597 GTGGCTAGTTCATTGCATGCAA 60.095 45.455 33.57 33.57 40.47 4.08
597 599 2.761767 TGGCTAGTTCATTGCATGCAAT 59.238 40.909 34.78 34.78 46.35 3.56
655 657 2.543777 TTTCCTCTTCCTTGGTCACG 57.456 50.000 0.00 0.00 0.00 4.35
656 658 0.685097 TTCCTCTTCCTTGGTCACGG 59.315 55.000 0.00 0.00 0.00 4.94
657 659 0.471211 TCCTCTTCCTTGGTCACGGT 60.471 55.000 0.00 0.00 0.00 4.83
658 660 0.320771 CCTCTTCCTTGGTCACGGTG 60.321 60.000 0.56 0.56 0.00 4.94
659 661 0.951040 CTCTTCCTTGGTCACGGTGC 60.951 60.000 2.51 0.00 0.00 5.01
660 662 1.227823 CTTCCTTGGTCACGGTGCA 60.228 57.895 2.51 0.00 0.00 4.57
661 663 0.606401 CTTCCTTGGTCACGGTGCAT 60.606 55.000 2.51 0.00 0.00 3.96
662 664 0.687920 TTCCTTGGTCACGGTGCATA 59.312 50.000 2.51 0.00 0.00 3.14
663 665 0.687920 TCCTTGGTCACGGTGCATAA 59.312 50.000 2.51 0.00 0.00 1.90
664 666 0.802494 CCTTGGTCACGGTGCATAAC 59.198 55.000 2.51 0.00 0.00 1.89
665 667 0.802494 CTTGGTCACGGTGCATAACC 59.198 55.000 2.51 6.52 46.60 2.85
678 680 6.846325 GGTGCATAACCTAAGATGACTTAC 57.154 41.667 0.00 0.00 46.55 2.34
679 681 6.583562 GGTGCATAACCTAAGATGACTTACT 58.416 40.000 0.00 0.00 46.55 2.24
680 682 6.702282 GGTGCATAACCTAAGATGACTTACTC 59.298 42.308 0.00 0.00 46.55 2.59
681 683 7.265673 GTGCATAACCTAAGATGACTTACTCA 58.734 38.462 0.00 0.00 37.53 3.41
682 684 7.222999 GTGCATAACCTAAGATGACTTACTCAC 59.777 40.741 0.00 0.00 37.53 3.51
683 685 6.418226 GCATAACCTAAGATGACTTACTCACG 59.582 42.308 0.00 0.00 37.53 4.35
684 686 5.979288 AACCTAAGATGACTTACTCACGT 57.021 39.130 0.00 0.00 37.53 4.49
685 687 8.618677 CATAACCTAAGATGACTTACTCACGTA 58.381 37.037 0.00 0.00 37.53 3.57
686 688 6.680874 ACCTAAGATGACTTACTCACGTAG 57.319 41.667 0.00 0.00 37.53 3.51
687 689 6.413052 ACCTAAGATGACTTACTCACGTAGA 58.587 40.000 0.00 0.00 37.53 2.59
688 690 7.055378 ACCTAAGATGACTTACTCACGTAGAT 58.945 38.462 0.00 0.00 37.53 1.98
689 691 7.012515 ACCTAAGATGACTTACTCACGTAGATG 59.987 40.741 0.00 0.00 37.53 2.90
690 692 5.759506 AGATGACTTACTCACGTAGATGG 57.240 43.478 0.00 0.00 0.00 3.51
691 693 5.437946 AGATGACTTACTCACGTAGATGGA 58.562 41.667 0.00 0.00 0.00 3.41
692 694 5.529430 AGATGACTTACTCACGTAGATGGAG 59.471 44.000 0.00 0.00 34.85 3.86
693 695 3.945921 TGACTTACTCACGTAGATGGAGG 59.054 47.826 5.03 0.00 32.98 4.30
694 696 3.288964 ACTTACTCACGTAGATGGAGGG 58.711 50.000 5.03 0.00 32.98 4.30
697 699 1.285373 ACTCACGTAGATGGAGGGAGT 59.715 52.381 5.03 0.00 32.98 3.85
708 710 9.021807 CGTAGATGGAGGGAGTAGATATTTAAA 57.978 37.037 0.00 0.00 0.00 1.52
955 958 1.738350 GTGTAGCTGAGACTAGTCGCA 59.262 52.381 25.09 25.09 37.07 5.10
960 963 0.380378 CTGAGACTAGTCGCAGGCTC 59.620 60.000 35.75 20.28 40.46 4.70
961 964 1.353804 GAGACTAGTCGCAGGCTCG 59.646 63.158 20.26 0.00 40.46 5.03
962 965 2.278271 GACTAGTCGCAGGCTCGC 60.278 66.667 7.22 0.00 40.46 5.03
963 966 3.052620 GACTAGTCGCAGGCTCGCA 62.053 63.158 7.22 0.00 40.46 5.10
964 967 2.278466 CTAGTCGCAGGCTCGCAG 60.278 66.667 9.10 3.28 40.46 5.18
965 968 2.750237 TAGTCGCAGGCTCGCAGA 60.750 61.111 9.10 5.12 40.46 4.26
990 993 3.311110 TTCTGCTTCCGCCGAGGT 61.311 61.111 0.00 0.00 41.99 3.85
1166 1187 1.543896 CTGGGAAGGGGAAGGGGAA 60.544 63.158 0.00 0.00 0.00 3.97
1225 1246 1.375326 GGACCGAAGCCCAAGAAGT 59.625 57.895 0.00 0.00 0.00 3.01
1266 1287 2.735134 GACGACGCAAAAGTTGGACTAT 59.265 45.455 0.00 0.00 0.00 2.12
1280 1301 1.002366 GACTATGTGCAGGACAAGCG 58.998 55.000 0.00 0.00 38.36 4.68
1296 1317 3.467119 CGTTTGTCCTCGCCGTCG 61.467 66.667 0.00 0.00 0.00 5.12
1350 1371 4.748798 CCTCCTCCACCCCTGCCT 62.749 72.222 0.00 0.00 0.00 4.75
1351 1372 3.406200 CTCCTCCACCCCTGCCTG 61.406 72.222 0.00 0.00 0.00 4.85
1354 1375 3.970410 CTCCACCCCTGCCTGCAA 61.970 66.667 0.00 0.00 0.00 4.08
1355 1376 4.284550 TCCACCCCTGCCTGCAAC 62.285 66.667 0.00 0.00 0.00 4.17
1441 1474 2.279851 CGTCTGCCCACGTTGTCA 60.280 61.111 0.00 0.00 34.95 3.58
1445 1478 1.227527 CTGCCCACGTTGTCAGACA 60.228 57.895 0.00 0.00 0.00 3.41
1498 1540 1.408340 TGACGGTTGAGGACGTTACAA 59.592 47.619 0.00 0.00 44.24 2.41
1656 1698 3.792736 GACGCTACCATGGCCCCA 61.793 66.667 13.04 0.00 0.00 4.96
1863 1905 2.227036 CCTTCAGGCCACCCTCAGT 61.227 63.158 5.01 0.00 40.33 3.41
1919 1961 2.282701 GTACGCATTCCTTGTACGGA 57.717 50.000 0.00 0.00 30.35 4.69
1920 1962 2.190981 GTACGCATTCCTTGTACGGAG 58.809 52.381 0.00 0.00 33.89 4.63
1921 1963 0.892755 ACGCATTCCTTGTACGGAGA 59.107 50.000 0.00 0.00 33.89 3.71
1922 1964 1.278238 CGCATTCCTTGTACGGAGAC 58.722 55.000 0.00 0.00 33.89 3.36
1923 1965 1.653151 GCATTCCTTGTACGGAGACC 58.347 55.000 0.00 0.00 33.89 3.85
2000 2042 7.438160 TGGTATTAATTTAGCAGTCATGACTCG 59.562 37.037 25.58 20.11 40.20 4.18
2043 2087 9.482175 ACTCTTATTATGAACTGAACTAGGAGT 57.518 33.333 0.00 0.00 0.00 3.85
2050 2094 9.616156 TTATGAACTGAACTAGGAGTAGAGTAG 57.384 37.037 0.00 0.00 0.00 2.57
2051 2095 7.018487 TGAACTGAACTAGGAGTAGAGTAGT 57.982 40.000 0.00 0.00 0.00 2.73
2052 2096 7.460071 TGAACTGAACTAGGAGTAGAGTAGTT 58.540 38.462 0.00 0.00 39.23 2.24
2053 2097 7.943447 TGAACTGAACTAGGAGTAGAGTAGTTT 59.057 37.037 0.00 0.00 37.17 2.66
2054 2098 9.447157 GAACTGAACTAGGAGTAGAGTAGTTTA 57.553 37.037 0.00 0.00 37.17 2.01
2055 2099 9.804977 AACTGAACTAGGAGTAGAGTAGTTTAA 57.195 33.333 0.00 0.00 37.17 1.52
2056 2100 9.452287 ACTGAACTAGGAGTAGAGTAGTTTAAG 57.548 37.037 0.00 0.00 37.17 1.85
2069 2113 6.154877 AGAGTAGTTTAAGTAAGAAGAGGGGC 59.845 42.308 0.00 0.00 0.00 5.80
2081 2125 1.823041 GAGGGGCAGAGATGCAAGC 60.823 63.158 2.29 0.00 36.33 4.01
2116 2161 2.484602 TCTAACAATGGTAGGGTCCCC 58.515 52.381 3.51 0.00 0.00 4.81
2117 2162 1.493446 CTAACAATGGTAGGGTCCCCC 59.507 57.143 3.51 0.00 45.90 5.40
2128 2173 1.353394 GGGTCCCCCAGATCGGATTT 61.353 60.000 0.00 0.00 44.65 2.17
2130 2175 0.179018 GTCCCCCAGATCGGATTTGG 60.179 60.000 18.21 18.21 36.56 3.28
2138 2183 0.843984 GATCGGATTTGGGGAGGGAA 59.156 55.000 0.00 0.00 0.00 3.97
2410 2459 3.239449 TCATGGTCGGTTCTGCCTATAT 58.761 45.455 0.00 0.00 34.25 0.86
2571 2721 0.893727 GTTGGCAATTGTCTCCGGGT 60.894 55.000 12.01 0.00 0.00 5.28
2588 2738 2.206576 GGTGAAAGCCTTGATCTGGT 57.793 50.000 0.00 0.00 0.00 4.00
2589 2739 1.815003 GGTGAAAGCCTTGATCTGGTG 59.185 52.381 0.00 0.00 0.00 4.17
2590 2740 1.200948 GTGAAAGCCTTGATCTGGTGC 59.799 52.381 0.00 0.00 0.00 5.01
2591 2741 1.074405 TGAAAGCCTTGATCTGGTGCT 59.926 47.619 0.00 0.00 0.00 4.40
2592 2742 1.471684 GAAAGCCTTGATCTGGTGCTG 59.528 52.381 0.00 0.00 31.55 4.41
2627 2777 0.948623 CGATGGCGGTGTCTTCAACA 60.949 55.000 0.00 0.00 34.78 3.33
2721 2873 1.625870 CTGCACGTAATCGCTCACG 59.374 57.895 0.00 0.00 43.63 4.35
2728 2880 0.455633 GTAATCGCTCACGTCGGTGT 60.456 55.000 0.00 0.00 44.68 4.16
2760 2913 0.038983 TCGCGGTGATTTCAAGACGA 60.039 50.000 6.13 0.00 0.00 4.20
2833 2987 1.410083 GCATTAAGGGAGGATGGTGCA 60.410 52.381 0.00 0.00 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
249 251 2.505777 CGCGCACCTCACTGAGAG 60.506 66.667 8.75 1.27 44.31 3.20
314 316 1.904771 CTGCCCCATCCGTAGAACA 59.095 57.895 0.00 0.00 0.00 3.18
401 403 1.212441 CACCTAGACGGAGGGAGTACT 59.788 57.143 0.00 0.00 41.36 2.73
402 404 1.064832 ACACCTAGACGGAGGGAGTAC 60.065 57.143 5.42 0.00 41.36 2.73
403 405 1.064906 CACACCTAGACGGAGGGAGTA 60.065 57.143 5.42 0.00 41.36 2.59
404 406 0.323542 CACACCTAGACGGAGGGAGT 60.324 60.000 5.42 1.31 41.36 3.85
405 407 0.323542 ACACACCTAGACGGAGGGAG 60.324 60.000 5.42 0.78 41.36 4.30
406 408 0.994247 TACACACCTAGACGGAGGGA 59.006 55.000 5.42 0.00 41.36 4.20
407 409 1.749634 CTTACACACCTAGACGGAGGG 59.250 57.143 5.42 0.00 41.36 4.30
408 410 2.422832 GACTTACACACCTAGACGGAGG 59.577 54.545 0.00 0.00 42.89 4.30
409 411 3.079578 TGACTTACACACCTAGACGGAG 58.920 50.000 0.00 0.00 36.31 4.63
410 412 3.144657 TGACTTACACACCTAGACGGA 57.855 47.619 0.00 0.00 36.31 4.69
411 413 3.695060 AGATGACTTACACACCTAGACGG 59.305 47.826 0.00 0.00 39.35 4.79
412 414 4.966965 AGATGACTTACACACCTAGACG 57.033 45.455 0.00 0.00 0.00 4.18
413 415 7.997482 TCATAAGATGACTTACACACCTAGAC 58.003 38.462 0.00 0.00 40.71 2.59
414 416 8.589701 TTCATAAGATGACTTACACACCTAGA 57.410 34.615 0.00 0.00 40.71 2.43
415 417 9.653287 TTTTCATAAGATGACTTACACACCTAG 57.347 33.333 0.00 0.00 40.71 3.02
416 418 9.431887 GTTTTCATAAGATGACTTACACACCTA 57.568 33.333 0.00 0.00 40.71 3.08
417 419 7.390718 GGTTTTCATAAGATGACTTACACACCT 59.609 37.037 0.00 0.00 40.71 4.00
418 420 7.174253 TGGTTTTCATAAGATGACTTACACACC 59.826 37.037 0.00 0.00 40.71 4.16
419 421 8.094798 TGGTTTTCATAAGATGACTTACACAC 57.905 34.615 0.00 0.00 40.71 3.82
420 422 8.684386 TTGGTTTTCATAAGATGACTTACACA 57.316 30.769 0.00 0.00 40.71 3.72
427 429 9.750125 GGGATTATTTGGTTTTCATAAGATGAC 57.250 33.333 0.00 0.00 39.39 3.06
428 430 9.486123 TGGGATTATTTGGTTTTCATAAGATGA 57.514 29.630 0.00 0.00 37.55 2.92
434 436 9.495572 GTGTTTTGGGATTATTTGGTTTTCATA 57.504 29.630 0.00 0.00 0.00 2.15
435 437 8.217111 AGTGTTTTGGGATTATTTGGTTTTCAT 58.783 29.630 0.00 0.00 0.00 2.57
436 438 7.569240 AGTGTTTTGGGATTATTTGGTTTTCA 58.431 30.769 0.00 0.00 0.00 2.69
437 439 8.445275 AAGTGTTTTGGGATTATTTGGTTTTC 57.555 30.769 0.00 0.00 0.00 2.29
438 440 9.554395 CTAAGTGTTTTGGGATTATTTGGTTTT 57.446 29.630 0.00 0.00 0.00 2.43
439 441 8.154203 CCTAAGTGTTTTGGGATTATTTGGTTT 58.846 33.333 0.00 0.00 0.00 3.27
440 442 7.676004 CCTAAGTGTTTTGGGATTATTTGGTT 58.324 34.615 0.00 0.00 0.00 3.67
441 443 6.295632 GCCTAAGTGTTTTGGGATTATTTGGT 60.296 38.462 0.00 0.00 30.91 3.67
442 444 6.106003 GCCTAAGTGTTTTGGGATTATTTGG 58.894 40.000 0.00 0.00 30.91 3.28
443 445 5.804979 CGCCTAAGTGTTTTGGGATTATTTG 59.195 40.000 0.00 0.00 30.91 2.32
444 446 5.623596 GCGCCTAAGTGTTTTGGGATTATTT 60.624 40.000 0.00 0.00 30.91 1.40
445 447 4.142249 GCGCCTAAGTGTTTTGGGATTATT 60.142 41.667 0.00 0.00 30.91 1.40
446 448 3.380320 GCGCCTAAGTGTTTTGGGATTAT 59.620 43.478 0.00 0.00 30.91 1.28
447 449 2.750712 GCGCCTAAGTGTTTTGGGATTA 59.249 45.455 0.00 0.00 30.91 1.75
448 450 1.544246 GCGCCTAAGTGTTTTGGGATT 59.456 47.619 0.00 0.00 30.91 3.01
449 451 1.173913 GCGCCTAAGTGTTTTGGGAT 58.826 50.000 0.00 0.00 30.91 3.85
450 452 1.231958 CGCGCCTAAGTGTTTTGGGA 61.232 55.000 0.00 0.00 30.91 4.37
451 453 1.209127 CGCGCCTAAGTGTTTTGGG 59.791 57.895 0.00 0.00 30.91 4.12
452 454 1.209127 CCGCGCCTAAGTGTTTTGG 59.791 57.895 0.00 0.00 33.04 3.28
453 455 0.385473 CACCGCGCCTAAGTGTTTTG 60.385 55.000 0.00 0.00 0.00 2.44
454 456 1.946267 CACCGCGCCTAAGTGTTTT 59.054 52.632 0.00 0.00 0.00 2.43
455 457 2.613506 GCACCGCGCCTAAGTGTTT 61.614 57.895 12.83 0.00 33.96 2.83
456 458 3.047877 GCACCGCGCCTAAGTGTT 61.048 61.111 12.83 0.00 33.96 3.32
457 459 3.605749 ATGCACCGCGCCTAAGTGT 62.606 57.895 12.83 0.00 41.33 3.55
458 460 1.087202 TAATGCACCGCGCCTAAGTG 61.087 55.000 0.00 4.02 41.33 3.16
459 461 0.391927 TTAATGCACCGCGCCTAAGT 60.392 50.000 0.00 0.00 41.33 2.24
460 462 0.730265 TTTAATGCACCGCGCCTAAG 59.270 50.000 0.00 0.00 41.33 2.18
461 463 1.384525 ATTTAATGCACCGCGCCTAA 58.615 45.000 0.00 0.00 41.33 2.69
462 464 1.384525 AATTTAATGCACCGCGCCTA 58.615 45.000 0.00 0.00 41.33 3.93
463 465 0.530288 AAATTTAATGCACCGCGCCT 59.470 45.000 0.00 0.00 41.33 5.52
464 466 1.355005 AAAATTTAATGCACCGCGCC 58.645 45.000 0.00 0.00 41.33 6.53
465 467 4.041723 AGATAAAATTTAATGCACCGCGC 58.958 39.130 0.00 0.00 42.89 6.86
466 468 4.375698 CGAGATAAAATTTAATGCACCGCG 59.624 41.667 0.00 0.00 0.00 6.46
467 469 5.270853 ACGAGATAAAATTTAATGCACCGC 58.729 37.500 0.00 0.00 0.00 5.68
468 470 7.734538 AAACGAGATAAAATTTAATGCACCG 57.265 32.000 0.00 0.00 0.00 4.94
491 493 9.829507 ATTGGTTGATATGTCAAGAAACAAAAA 57.170 25.926 4.98 0.00 44.58 1.94
495 497 9.513906 TCTTATTGGTTGATATGTCAAGAAACA 57.486 29.630 4.98 0.63 44.58 2.83
506 508 7.890127 CACCCCACATATCTTATTGGTTGATAT 59.110 37.037 0.00 0.00 34.77 1.63
507 509 7.147213 ACACCCCACATATCTTATTGGTTGATA 60.147 37.037 0.00 0.00 0.00 2.15
508 510 6.070656 CACCCCACATATCTTATTGGTTGAT 58.929 40.000 0.00 0.00 0.00 2.57
509 511 5.044476 ACACCCCACATATCTTATTGGTTGA 60.044 40.000 0.00 0.00 0.00 3.18
510 512 5.200483 ACACCCCACATATCTTATTGGTTG 58.800 41.667 0.00 0.00 0.00 3.77
511 513 5.466127 ACACCCCACATATCTTATTGGTT 57.534 39.130 0.00 0.00 0.00 3.67
512 514 5.430417 TGTACACCCCACATATCTTATTGGT 59.570 40.000 0.00 0.00 0.00 3.67
513 515 5.935945 TGTACACCCCACATATCTTATTGG 58.064 41.667 0.00 0.00 0.00 3.16
514 516 6.998074 ACATGTACACCCCACATATCTTATTG 59.002 38.462 0.00 0.00 34.88 1.90
515 517 7.149202 ACATGTACACCCCACATATCTTATT 57.851 36.000 0.00 0.00 34.88 1.40
516 518 6.763715 ACATGTACACCCCACATATCTTAT 57.236 37.500 0.00 0.00 34.88 1.73
517 519 6.569127 AACATGTACACCCCACATATCTTA 57.431 37.500 0.00 0.00 34.88 2.10
518 520 5.450818 AACATGTACACCCCACATATCTT 57.549 39.130 0.00 0.00 34.88 2.40
519 521 5.450818 AAACATGTACACCCCACATATCT 57.549 39.130 0.00 0.00 34.88 1.98
520 522 6.524101 AAAAACATGTACACCCCACATATC 57.476 37.500 0.00 0.00 34.88 1.63
521 523 8.474025 CATTAAAAACATGTACACCCCACATAT 58.526 33.333 0.00 0.00 34.88 1.78
522 524 7.670140 TCATTAAAAACATGTACACCCCACATA 59.330 33.333 0.00 0.00 34.88 2.29
523 525 6.495181 TCATTAAAAACATGTACACCCCACAT 59.505 34.615 0.00 0.00 37.09 3.21
524 526 5.833667 TCATTAAAAACATGTACACCCCACA 59.166 36.000 0.00 0.00 0.00 4.17
525 527 6.015772 AGTCATTAAAAACATGTACACCCCAC 60.016 38.462 0.00 0.00 0.00 4.61
526 528 6.071984 AGTCATTAAAAACATGTACACCCCA 58.928 36.000 0.00 0.00 0.00 4.96
527 529 6.584185 AGTCATTAAAAACATGTACACCCC 57.416 37.500 0.00 0.00 0.00 4.95
528 530 7.653647 TCAAGTCATTAAAAACATGTACACCC 58.346 34.615 0.00 0.00 0.00 4.61
529 531 8.564574 TCTCAAGTCATTAAAAACATGTACACC 58.435 33.333 0.00 0.00 0.00 4.16
530 532 9.382244 GTCTCAAGTCATTAAAAACATGTACAC 57.618 33.333 0.00 0.00 0.00 2.90
531 533 9.337396 AGTCTCAAGTCATTAAAAACATGTACA 57.663 29.630 0.00 0.00 0.00 2.90
534 536 8.784043 GGTAGTCTCAAGTCATTAAAAACATGT 58.216 33.333 0.00 0.00 0.00 3.21
535 537 8.783093 TGGTAGTCTCAAGTCATTAAAAACATG 58.217 33.333 0.00 0.00 0.00 3.21
536 538 8.918202 TGGTAGTCTCAAGTCATTAAAAACAT 57.082 30.769 0.00 0.00 0.00 2.71
537 539 8.740123 TTGGTAGTCTCAAGTCATTAAAAACA 57.260 30.769 0.00 0.00 0.00 2.83
538 540 9.447040 GTTTGGTAGTCTCAAGTCATTAAAAAC 57.553 33.333 0.00 0.00 0.00 2.43
539 541 9.179909 TGTTTGGTAGTCTCAAGTCATTAAAAA 57.820 29.630 0.00 0.00 0.00 1.94
540 542 8.617809 GTGTTTGGTAGTCTCAAGTCATTAAAA 58.382 33.333 0.00 0.00 0.00 1.52
541 543 7.042321 CGTGTTTGGTAGTCTCAAGTCATTAAA 60.042 37.037 0.00 0.00 0.00 1.52
542 544 6.422701 CGTGTTTGGTAGTCTCAAGTCATTAA 59.577 38.462 0.00 0.00 0.00 1.40
543 545 5.924254 CGTGTTTGGTAGTCTCAAGTCATTA 59.076 40.000 0.00 0.00 0.00 1.90
544 546 4.750098 CGTGTTTGGTAGTCTCAAGTCATT 59.250 41.667 0.00 0.00 0.00 2.57
545 547 4.038763 TCGTGTTTGGTAGTCTCAAGTCAT 59.961 41.667 0.00 0.00 0.00 3.06
546 548 3.382227 TCGTGTTTGGTAGTCTCAAGTCA 59.618 43.478 0.00 0.00 0.00 3.41
547 549 3.734735 GTCGTGTTTGGTAGTCTCAAGTC 59.265 47.826 0.00 0.00 0.00 3.01
548 550 3.131577 TGTCGTGTTTGGTAGTCTCAAGT 59.868 43.478 0.00 0.00 0.00 3.16
549 551 3.713288 TGTCGTGTTTGGTAGTCTCAAG 58.287 45.455 0.00 0.00 0.00 3.02
550 552 3.804786 TGTCGTGTTTGGTAGTCTCAA 57.195 42.857 0.00 0.00 0.00 3.02
551 553 3.649073 CATGTCGTGTTTGGTAGTCTCA 58.351 45.455 0.00 0.00 0.00 3.27
552 554 2.412089 GCATGTCGTGTTTGGTAGTCTC 59.588 50.000 0.00 0.00 0.00 3.36
553 555 2.224185 TGCATGTCGTGTTTGGTAGTCT 60.224 45.455 0.00 0.00 0.00 3.24
554 556 2.139917 TGCATGTCGTGTTTGGTAGTC 58.860 47.619 0.00 0.00 0.00 2.59
555 557 2.143122 CTGCATGTCGTGTTTGGTAGT 58.857 47.619 0.00 0.00 0.00 2.73
556 558 2.096268 CACTGCATGTCGTGTTTGGTAG 60.096 50.000 7.95 0.00 0.00 3.18
557 559 1.870402 CACTGCATGTCGTGTTTGGTA 59.130 47.619 7.95 0.00 0.00 3.25
558 560 0.662619 CACTGCATGTCGTGTTTGGT 59.337 50.000 7.95 0.00 0.00 3.67
559 561 0.040157 CCACTGCATGTCGTGTTTGG 60.040 55.000 13.12 0.00 0.00 3.28
560 562 0.661187 GCCACTGCATGTCGTGTTTG 60.661 55.000 13.12 2.84 37.47 2.93
561 563 0.819259 AGCCACTGCATGTCGTGTTT 60.819 50.000 13.12 1.83 41.13 2.83
562 564 0.034756 TAGCCACTGCATGTCGTGTT 59.965 50.000 13.12 6.12 41.13 3.32
563 565 0.390340 CTAGCCACTGCATGTCGTGT 60.390 55.000 13.12 2.00 41.13 4.49
564 566 0.390340 ACTAGCCACTGCATGTCGTG 60.390 55.000 8.87 8.87 41.13 4.35
565 567 0.321671 AACTAGCCACTGCATGTCGT 59.678 50.000 0.00 0.00 41.13 4.34
566 568 1.002366 GAACTAGCCACTGCATGTCG 58.998 55.000 0.00 0.00 41.13 4.35
567 569 2.099141 TGAACTAGCCACTGCATGTC 57.901 50.000 0.00 0.00 41.13 3.06
568 570 2.751259 CAATGAACTAGCCACTGCATGT 59.249 45.455 0.00 0.00 41.13 3.21
569 571 2.479049 GCAATGAACTAGCCACTGCATG 60.479 50.000 12.41 0.00 36.83 4.06
570 572 1.747355 GCAATGAACTAGCCACTGCAT 59.253 47.619 12.41 0.00 36.83 3.96
571 573 1.167851 GCAATGAACTAGCCACTGCA 58.832 50.000 12.41 0.00 36.83 4.41
572 574 1.167851 TGCAATGAACTAGCCACTGC 58.832 50.000 10.92 10.92 37.29 4.40
634 636 3.211045 CGTGACCAAGGAAGAGGAAAAA 58.789 45.455 0.00 0.00 0.00 1.94
635 637 2.486548 CCGTGACCAAGGAAGAGGAAAA 60.487 50.000 0.00 0.00 31.21 2.29
636 638 1.071699 CCGTGACCAAGGAAGAGGAAA 59.928 52.381 0.00 0.00 31.21 3.13
637 639 0.685097 CCGTGACCAAGGAAGAGGAA 59.315 55.000 0.00 0.00 31.21 3.36
638 640 0.471211 ACCGTGACCAAGGAAGAGGA 60.471 55.000 8.91 0.00 33.97 3.71
639 641 0.320771 CACCGTGACCAAGGAAGAGG 60.321 60.000 8.91 0.00 33.97 3.69
640 642 0.951040 GCACCGTGACCAAGGAAGAG 60.951 60.000 8.91 0.00 33.97 2.85
641 643 1.070786 GCACCGTGACCAAGGAAGA 59.929 57.895 8.91 0.00 33.97 2.87
642 644 0.606401 ATGCACCGTGACCAAGGAAG 60.606 55.000 8.91 2.67 33.97 3.46
643 645 0.687920 TATGCACCGTGACCAAGGAA 59.312 50.000 8.91 0.00 33.97 3.36
644 646 0.687920 TTATGCACCGTGACCAAGGA 59.312 50.000 8.91 0.00 33.97 3.36
645 647 0.802494 GTTATGCACCGTGACCAAGG 59.198 55.000 1.65 0.44 35.99 3.61
646 648 0.802494 GGTTATGCACCGTGACCAAG 59.198 55.000 1.65 0.00 35.12 3.61
647 649 2.935505 GGTTATGCACCGTGACCAA 58.064 52.632 1.65 0.00 35.12 3.67
648 650 4.705746 GGTTATGCACCGTGACCA 57.294 55.556 1.65 0.00 35.12 4.02
651 653 8.981918 TAAGTCATCTTAGGTTATGCACCGTGA 61.982 40.741 1.65 0.00 41.54 4.35
652 654 6.903183 TAAGTCATCTTAGGTTATGCACCGTG 60.903 42.308 0.00 0.00 41.54 4.94
653 655 5.128171 TAAGTCATCTTAGGTTATGCACCGT 59.872 40.000 0.00 0.00 41.54 4.83
654 656 5.462398 GTAAGTCATCTTAGGTTATGCACCG 59.538 44.000 0.00 0.00 41.54 4.94
655 657 6.583562 AGTAAGTCATCTTAGGTTATGCACC 58.416 40.000 0.00 0.00 39.22 5.01
656 658 7.222999 GTGAGTAAGTCATCTTAGGTTATGCAC 59.777 40.741 0.00 0.00 37.56 4.57
657 659 7.265673 GTGAGTAAGTCATCTTAGGTTATGCA 58.734 38.462 0.00 0.00 37.56 3.96
658 660 6.418226 CGTGAGTAAGTCATCTTAGGTTATGC 59.582 42.308 0.00 0.00 37.56 3.14
659 661 7.481642 ACGTGAGTAAGTCATCTTAGGTTATG 58.518 38.462 0.00 0.00 46.88 1.90
660 662 7.642082 ACGTGAGTAAGTCATCTTAGGTTAT 57.358 36.000 0.00 0.00 46.88 1.89
662 664 5.979288 ACGTGAGTAAGTCATCTTAGGTT 57.021 39.130 0.00 0.00 46.88 3.50
676 678 2.508716 ACTCCCTCCATCTACGTGAGTA 59.491 50.000 0.00 0.00 46.88 2.59
678 680 2.060050 ACTCCCTCCATCTACGTGAG 57.940 55.000 0.00 0.00 0.00 3.51
679 681 2.775960 TCTACTCCCTCCATCTACGTGA 59.224 50.000 0.00 0.00 0.00 4.35
680 682 3.210232 TCTACTCCCTCCATCTACGTG 57.790 52.381 0.00 0.00 0.00 4.49
681 683 5.782677 ATATCTACTCCCTCCATCTACGT 57.217 43.478 0.00 0.00 0.00 3.57
682 684 8.577048 TTAAATATCTACTCCCTCCATCTACG 57.423 38.462 0.00 0.00 0.00 3.51
685 687 9.052365 GGATTTAAATATCTACTCCCTCCATCT 57.948 37.037 0.00 0.00 0.00 2.90
686 688 7.982354 CGGATTTAAATATCTACTCCCTCCATC 59.018 40.741 0.00 0.00 0.00 3.51
687 689 7.581658 GCGGATTTAAATATCTACTCCCTCCAT 60.582 40.741 0.00 0.00 0.00 3.41
688 690 6.295688 GCGGATTTAAATATCTACTCCCTCCA 60.296 42.308 0.00 0.00 0.00 3.86
689 691 6.070710 AGCGGATTTAAATATCTACTCCCTCC 60.071 42.308 0.00 0.00 0.00 4.30
690 692 6.937392 AGCGGATTTAAATATCTACTCCCTC 58.063 40.000 0.00 0.00 0.00 4.30
691 693 6.936968 AGCGGATTTAAATATCTACTCCCT 57.063 37.500 0.00 0.00 0.00 4.20
692 694 6.128254 GCAAGCGGATTTAAATATCTACTCCC 60.128 42.308 0.00 0.00 0.00 4.30
693 695 6.401153 CGCAAGCGGATTTAAATATCTACTCC 60.401 42.308 6.55 0.00 35.56 3.85
694 696 6.145696 ACGCAAGCGGATTTAAATATCTACTC 59.854 38.462 19.30 0.00 44.69 2.59
697 699 5.333798 GCACGCAAGCGGATTTAAATATCTA 60.334 40.000 19.30 0.00 44.69 1.98
934 937 1.064357 GCGACTAGTCTCAGCTACACC 59.936 57.143 20.34 0.00 0.00 4.16
955 958 2.259818 CAGAACGTCTGCGAGCCT 59.740 61.111 0.00 0.00 37.72 4.58
963 966 1.603172 CGGAAGCAGAACAGAACGTCT 60.603 52.381 0.00 0.00 0.00 4.18
964 967 0.784778 CGGAAGCAGAACAGAACGTC 59.215 55.000 0.00 0.00 0.00 4.34
965 968 2.900528 CGGAAGCAGAACAGAACGT 58.099 52.632 0.00 0.00 0.00 3.99
990 993 1.136891 CTCTCCATCATACACCACGCA 59.863 52.381 0.00 0.00 0.00 5.24
1166 1187 2.978010 CTGCAACCGCCTTCCGTT 60.978 61.111 0.00 0.00 37.32 4.44
1194 1215 2.689034 GGTCCCCTCCTCCCAGTG 60.689 72.222 0.00 0.00 0.00 3.66
1211 1232 2.391389 GCCGACTTCTTGGGCTTCG 61.391 63.158 0.00 0.00 43.52 3.79
1266 1287 1.029408 ACAAACGCTTGTCCTGCACA 61.029 50.000 0.00 0.00 42.25 4.57
1280 1301 2.355481 ACGACGGCGAGGACAAAC 60.355 61.111 22.49 0.00 41.64 2.93
1296 1317 2.123812 ATCCCCGACGAGGAGGAC 60.124 66.667 3.91 0.00 45.00 3.85
1352 1373 3.818787 GCATGAGCGGCAGGGTTG 61.819 66.667 1.45 0.00 0.00 3.77
1426 1459 1.069090 GTCTGACAACGTGGGCAGA 59.931 57.895 25.19 25.19 32.92 4.26
1863 1905 4.761058 AAGCCGCCGAGGGAGAGA 62.761 66.667 0.00 0.00 41.48 3.10
1917 1959 0.465097 TCATACGTCTCCCGGTCTCC 60.465 60.000 0.00 0.00 42.24 3.71
1918 1960 1.065251 GTTCATACGTCTCCCGGTCTC 59.935 57.143 0.00 0.00 42.24 3.36
1919 1961 1.101331 GTTCATACGTCTCCCGGTCT 58.899 55.000 0.00 0.00 42.24 3.85
1920 1962 0.101939 GGTTCATACGTCTCCCGGTC 59.898 60.000 0.00 0.00 42.24 4.79
1921 1963 0.612732 TGGTTCATACGTCTCCCGGT 60.613 55.000 0.00 0.00 42.24 5.28
1922 1964 0.533491 TTGGTTCATACGTCTCCCGG 59.467 55.000 0.00 0.00 42.24 5.73
1923 1965 2.159156 TGATTGGTTCATACGTCTCCCG 60.159 50.000 0.00 0.00 44.03 5.14
1924 1966 3.536956 TGATTGGTTCATACGTCTCCC 57.463 47.619 0.00 0.00 0.00 4.30
2041 2085 9.465199 CCCTCTTCTTACTTAAACTACTCTACT 57.535 37.037 0.00 0.00 0.00 2.57
2042 2086 8.685427 CCCCTCTTCTTACTTAAACTACTCTAC 58.315 40.741 0.00 0.00 0.00 2.59
2043 2087 7.341512 GCCCCTCTTCTTACTTAAACTACTCTA 59.658 40.741 0.00 0.00 0.00 2.43
2045 2089 6.070938 TGCCCCTCTTCTTACTTAAACTACTC 60.071 42.308 0.00 0.00 0.00 2.59
2046 2090 5.783875 TGCCCCTCTTCTTACTTAAACTACT 59.216 40.000 0.00 0.00 0.00 2.57
2047 2091 6.046290 TGCCCCTCTTCTTACTTAAACTAC 57.954 41.667 0.00 0.00 0.00 2.73
2048 2092 6.021030 TCTGCCCCTCTTCTTACTTAAACTA 58.979 40.000 0.00 0.00 0.00 2.24
2049 2093 4.844655 TCTGCCCCTCTTCTTACTTAAACT 59.155 41.667 0.00 0.00 0.00 2.66
2050 2094 5.046520 TCTCTGCCCCTCTTCTTACTTAAAC 60.047 44.000 0.00 0.00 0.00 2.01
2051 2095 5.091552 TCTCTGCCCCTCTTCTTACTTAAA 58.908 41.667 0.00 0.00 0.00 1.52
2052 2096 4.684724 TCTCTGCCCCTCTTCTTACTTAA 58.315 43.478 0.00 0.00 0.00 1.85
2053 2097 4.332683 TCTCTGCCCCTCTTCTTACTTA 57.667 45.455 0.00 0.00 0.00 2.24
2054 2098 3.191888 TCTCTGCCCCTCTTCTTACTT 57.808 47.619 0.00 0.00 0.00 2.24
2055 2099 2.930109 TCTCTGCCCCTCTTCTTACT 57.070 50.000 0.00 0.00 0.00 2.24
2056 2100 2.484594 GCATCTCTGCCCCTCTTCTTAC 60.485 54.545 0.00 0.00 42.88 2.34
2081 2125 7.382218 ACCATTGTTAGAAAGAAATCTTTTGCG 59.618 33.333 9.60 1.20 45.37 4.85
2116 2161 0.109342 CCTCCCCAAATCCGATCTGG 59.891 60.000 0.00 0.00 40.09 3.86
2117 2162 0.109342 CCCTCCCCAAATCCGATCTG 59.891 60.000 0.00 0.00 0.00 2.90
2118 2163 0.030092 TCCCTCCCCAAATCCGATCT 60.030 55.000 0.00 0.00 0.00 2.75
2119 2164 0.843984 TTCCCTCCCCAAATCCGATC 59.156 55.000 0.00 0.00 0.00 3.69
2120 2165 0.846693 CTTCCCTCCCCAAATCCGAT 59.153 55.000 0.00 0.00 0.00 4.18
2121 2166 0.549169 ACTTCCCTCCCCAAATCCGA 60.549 55.000 0.00 0.00 0.00 4.55
2128 2173 2.935481 CCAGCACTTCCCTCCCCA 60.935 66.667 0.00 0.00 0.00 4.96
2130 2175 4.432741 GGCCAGCACTTCCCTCCC 62.433 72.222 0.00 0.00 0.00 4.30
2138 2183 1.630126 AATCCGATCTGGCCAGCACT 61.630 55.000 28.91 14.80 37.80 4.40
2327 2376 4.452733 GCAACCGAGGTCCTCCCG 62.453 72.222 13.54 6.21 38.74 5.14
2410 2459 2.725312 GCATCTCCGCACCTCCAGA 61.725 63.158 0.00 0.00 0.00 3.86
2571 2721 1.074405 AGCACCAGATCAAGGCTTTCA 59.926 47.619 0.00 0.00 0.00 2.69
2590 2740 4.100084 TGCCGATCCAGCACCCAG 62.100 66.667 1.02 0.00 34.69 4.45
2617 2767 2.029020 CAGAGGGACGATGTTGAAGACA 60.029 50.000 0.00 0.00 43.71 3.41
2709 2860 0.455633 ACACCGACGTGAGCGATTAC 60.456 55.000 0.00 0.00 43.14 1.89
2721 2873 3.722780 CGAAGATCGTACATAACACCGAC 59.277 47.826 0.00 0.00 34.72 4.79
2728 2880 2.355444 TCACCGCGAAGATCGTACATAA 59.645 45.455 8.23 0.00 42.81 1.90
2760 2913 0.323542 ATCTGACCCGAGGAAGACGT 60.324 55.000 0.00 0.00 0.00 4.34


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.